Variant report

Variant	rs7541543
Chromosome Location	chr1:215293924-215293925
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:215293562..215295636-chr1:215380314..215382077,2	K562	blood:
2	chr1:215285008..215287414-chr1:215293521..215295333,2	MCF-7	breast:
3	chr1:215293174..215295658-chr1:215298040..215300883,2	K562	blood:

Extended variants
information (count: 134 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs10127521	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10127656	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10746454	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10746455	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10779639	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10779640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10779642	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10779643	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10779644	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10779645	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10779646	0.90[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs10779647	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10779648	0.89[ASN][1000 genomes]
rs10779649	0.89[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10779650	0.90[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs10779651	0.90[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.87[YRI][hapmap];0.83[ASN][1000 genomes]
rs10864150	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[YRI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10864152	0.95[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10864153	0.95[ASN][1000 genomes]
rs10864154	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11120495	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11120496	0.97[ASN][1000 genomes]
rs11120497	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11120498	0.98[ASN][1000 genomes]
rs11120499	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11120500	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11120506	0.96[ASN][1000 genomes]
rs11120508	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11120511	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11120513	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11120516	0.96[ASN][1000 genomes]
rs11120517	0.92[ASN][1000 genomes]
rs1112101	0.89[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];0.95[YRI][hapmap];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12031308	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12039875	0.80[CHB][hapmap];0.87[CHD][hapmap]
rs12061916	0.98[ASN][1000 genomes]
rs12068734	0.96[ASN][1000 genomes]
rs12120091	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12121761	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12135076	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12138497	0.83[ASN][1000 genomes]
rs12141874	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12143339	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12410041	0.83[CEU][hapmap];0.90[CHB][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12411068	0.85[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs12567520	0.80[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.85[ASN][1000 genomes]
rs12742137	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1339405	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1339406	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1361340	0.87[ASW][hapmap];0.87[CHD][hapmap];0.89[MKK][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1416647	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1538547	0.85[CHB][hapmap]
rs1556906	0.83[YRI][hapmap]
rs1578137	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2363552	0.81[YRI][hapmap]
rs2363554	0.94[CHB][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs2363556	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2363557	0.89[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.84[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2363558	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2363559	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2363560	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2363564	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2363565	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2363566	0.89[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2363567	0.87[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.87[TSI][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2885812	1.00[CHB][hapmap];0.96[ASN][1000 genomes]
rs2885813	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2885815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3931584	0.95[ASN][1000 genomes]
rs4233309	0.85[CHB][hapmap];0.82[CHD][hapmap]
rs4262516	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4269745	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4271184	0.95[CHB][hapmap];0.95[CHD][hapmap]
rs4300189	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4303048	0.89[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4375232	0.90[CEU][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4394614	0.92[ASN][1000 genomes]
rs4411107	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4428856	0.98[ASN][1000 genomes]
rs4440833	0.92[ASN][1000 genomes]
rs4497183	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4509552	0.96[ASN][1000 genomes]
rs4509553	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4531266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4548407	0.88[AMR][1000 genomes]
rs4556330	0.95[CHB][hapmap]
rs4571941	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4573492	0.98[ASN][1000 genomes]
rs4607848	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4634877	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs4655276	0.96[ASN][1000 genomes]
rs4655277	0.90[CHB][hapmap];0.81[JPT][hapmap];0.87[YRI][hapmap];0.83[ASN][1000 genomes]
rs4655278	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4655391	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4655392	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4655393	0.90[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4655394	0.90[CHB][hapmap];0.90[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs4655395	0.90[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61818297	0.83[AMR][1000 genomes]
rs61818299	0.83[AMR][1000 genomes]
rs61818320	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61818328	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6540887	0.84[JPT][hapmap]
rs6657313	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6662353	1.00[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6666828	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6667764	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6672978	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6673739	0.81[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs6675926	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6678758	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6683041	0.98[ASN][1000 genomes]
rs6684084	0.90[CHB][hapmap];0.92[CHD][hapmap];0.87[YRI][hapmap];0.83[ASN][1000 genomes]
rs6688713	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6695967	0.93[CEU][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6696333	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6699161	0.85[CHB][hapmap];0.90[CHD][hapmap]
rs72735359	0.84[ASN][1000 genomes]
rs7410928	0.80[AMR][1000 genomes]
rs7417100	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7513709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7516689	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7535436	0.81[YRI][hapmap]
rs7540029	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7547572	0.90[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs7547655	0.95[CEU][hapmap];0.80[CHD][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes]
rs7549136	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7551415	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7551562	0.81[YRI][hapmap]
rs7555013	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7555727	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9793690	0.85[AMR][1000 genomes]
rs9793695	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873169	chr1:215264486-215453286	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	Chromatin interactive region miRNA target site	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7541543	SYT14	cis	parietal	SCAN
rs7541543	FDX1	trans	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:215288200-215294000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:215288800-215306600	Weak transcription	NHLF	lung
3	chr1:215291600-215300400	Weak transcription	Osteobl	bone
4	chr1:215292600-215294000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:215292600-215294600	Enhancers	NHDF-Ad	bronchial
6	chr1:215293600-215294200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:215293800-215294000	Enhancers	Hela-S3	cervix
8	chr1:215293800-215298600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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